Contacts of the helix formed by residues 30 - 55 (chain A) in PDB entry 3KAV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 1.3 74.2 - - - +
31A GLN* 1.3 55.3 + - - +
32A ALA 3.3 4.5 - - - -
33A PRO* 3.4 25.0 - - + +
34A GLU* 4.0 8.7 + - - +
83A ARG* 6.0 1.6 - - - -
129A LEU* 5.2 1.9 - - - +
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 2.7 23.9 + - - +
30A ALA* 1.3 77.9 - - - +
32A ALA* 1.3 58.8 + - - +
33A PRO 3.6 0.2 - - - -
34A GLU* 3.9 18.2 - - - +
35A GLU* 3.1 28.8 + - - +
83A ARG* 3.0 33.0 - - - +
53D ALA 4.2 0.4 - - - -
54D LEU* 3.4 40.2 + - + +
56D THR* 3.9 2.7 - - + +
111D LEU* 3.8 21.1 - - - +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 3.5 6.2 + - - +
31A GLN* 1.3 75.9 - - - +
33A PRO* 1.3 73.8 - - + +
35A GLU* 3.2 3.8 + - - +
36A ARG* 3.0 45.1 + - - +
53D ALA* 3.4 18.5 - - + +
54D LEU* 3.9 15.2 - - + +
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Residues in contact with PRO 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 4.6 0.2 - - - +
30A ALA* 3.4 24.0 - - + +
32A ALA* 1.3 97.9 - - + +
34A GLU* 1.3 57.9 + - - +
36A ARG* 2.9 43.0 - - - +
37A CYS* 3.0 15.1 + - - +
125A ALA 4.5 1.2 - - - +
128A PRO* 4.1 28.7 - - + -
129A LEU* 3.7 8.4 - - + +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 4.0 11.0 - - - +
31A GLN* 4.0 7.5 - - - +
32A ALA 3.2 0.6 - - - -
33A PRO* 1.3 83.6 - - - +
35A GLU* 1.3 52.0 + - - +
37A CYS 3.2 0.2 + - - -
38A ARG* 2.8 31.0 + - - +
80A MSE 3.1 60.4 - - + +
83A ARG* 2.9 42.0 + - - -
84A SER 4.9 1.6 - - - +
87A ALA* 4.0 10.0 - - - +
129A LEU* 3.4 16.3 - - + +
56D THR* 3.8 7.6 - - + +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN 3.1 19.9 + - - +
32A ALA 3.2 4.4 + - - +
34A GLU* 1.3 74.1 - - - +
36A ARG* 1.3 60.4 + - - +
38A ARG* 3.1 31.6 + - - -
39A LEU* 3.0 48.6 + - + +
52D LEU 4.1 12.0 - - - +
53D ALA* 3.6 15.5 - - - +
55D CYS 3.0 26.9 - - - +
56D THR* 3.1 12.4 - - + -
58D SER* 4.1 6.8 + - - -
63D ARG* 4.2 3.6 + - - -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 3.0 39.1 + - - +
33A PRO* 2.9 41.9 - - - +
35A GLU* 1.3 79.7 - - - +
37A CYS* 1.3 58.0 + - + +
39A LEU* 3.6 9.4 + - - +
40A ALA* 3.0 26.5 + - - +
125A ALA* 4.4 10.5 - - + +
128A PRO* 5.8 2.9 - - - +
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 3.0 20.0 + - - +
35A GLU 3.1 0.2 - - - -
36A ARG* 1.3 75.8 - - - +
38A ARG* 1.3 59.2 + - - +
40A ALA* 3.1 2.3 + - - +
41A ALA* 2.8 30.8 + - - +
80A MSE 3.3 23.6 - - + -
91A CYS* 4.2 3.1 - - - -
122A PHE* 3.9 6.9 - - - -
125A ALA* 3.7 23.1 - - - +
126A CYS* 3.8 26.2 - - - -
129A LEU* 3.4 19.7 - - + -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU 2.8 16.3 + - - +
35A GLU* 3.1 34.1 + - - +
37A CYS* 1.3 77.6 - - - +
39A LEU* 1.3 65.6 + - - +
41A ALA* 3.3 6.6 + - - +
42A GLN* 2.9 60.4 + - - +
77A ALA* 3.8 22.8 - - - +
80A MSE 3.6 19.5 - - + -
81A GLU* 3.4 22.7 + - - +
56D THR* 3.0 31.5 + - - +
57D GLU* 4.4 3.0 - - - +
58D SER* 3.0 31.7 + - - +
59D SER* 5.4 0.8 - - - +
60D ARG* 5.6 2.2 - - - +
63D ARG* 4.2 1.0 - - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.0 42.8 + - + +
36A ARG* 3.9 7.9 - - - +
38A ARG* 1.3 85.5 - - - +
40A ALA* 1.3 65.7 + - - +
42A GLN* 3.3 25.0 + - - +
43A ALA* 3.0 23.0 + - - +
46A ARG* 5.0 0.9 + - - -
63D ARG* 3.6 35.9 - - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 3.0 18.6 + - - +
37A CYS 3.1 4.9 + - - +
39A LEU* 1.3 76.3 - - - +
41A ALA* 1.3 63.8 + - - +
43A ALA* 3.1 8.1 + - - +
44A CYS* 2.9 23.2 + - - +
118A ALA 5.0 1.0 - - - +
121A ARG* 4.5 4.7 - - + +
122A PHE* 3.8 28.2 - - - +
125A ALA* 3.9 12.3 - - + -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A CYS 2.8 10.1 + - - +
38A ARG* 3.4 12.3 - - - +
40A ALA* 1.3 76.2 - - - +
42A GLN* 1.3 62.1 + - - +
44A CYS* 3.0 14.4 + - - +
45A ILE* 3.0 20.0 + - - +
73A CYS* 4.0 21.9 - - - +
76A ALA* 5.3 1.8 - - + -
77A ALA* 4.5 8.1 - - + +
80A MSE 5.6 1.1 - - - -
122A PHE* 3.4 32.2 - - + -
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG* 2.9 46.5 + - - +
39A LEU* 3.4 29.9 + - - +
40A ALA 3.2 0.2 - - - -
41A ALA* 1.3 76.4 - - - +
43A ALA* 1.3 62.2 + - - +
45A ILE* 3.2 31.4 - - + +
46A ARG* 3.2 33.2 + - - +
77A ALA* 4.5 10.7 - - + +
81A GLU* 3.4 10.2 - - - +
60D ARG* 5.2 11.1 + - - +
63D ARG* 4.2 7.3 - - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 3.0 12.9 + - - +
40A ALA* 3.1 10.3 + - - +
42A GLN* 1.3 76.0 - - - +
44A CYS* 1.3 62.8 + - - +
46A ARG* 3.2 24.4 + - - +
47A ALA* 3.0 23.4 + - - +
50A ARG* 4.7 1.9 + - - -
118A ALA* 4.3 6.6 - - + +
121A ARG* 6.2 1.6 - - - +
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Residues in contact with CYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 2.9 12.6 + - - +
41A ALA 3.3 10.3 - - - +
43A ALA* 1.3 77.9 - - - +
45A ILE* 1.3 57.4 + - - +
47A ALA* 3.4 2.4 + - - +
48A CYS* 3.0 32.4 + - - -
69A CYS* 3.5 31.6 - - - -
73A CYS* 3.8 12.8 - - - -
118A ALA* 3.9 13.2 - - - +
119A CYS* 3.6 28.7 - - - -
122A PHE* 4.1 12.3 - - + -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 3.0 15.9 + - - +
42A GLN* 3.2 18.2 - - + +
44A CYS* 1.3 75.8 - - - +
46A ARG* 1.3 68.5 + - + +
48A CYS* 3.1 7.0 + - - +
49A GLU* 2.8 41.8 + - + +
70A ALA* 3.8 20.0 - - + +
73A CYS* 3.4 28.9 - - + -
74A ARG* 3.7 42.2 - - + +
77A ALA* 6.3 0.4 - - + -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 5.0 0.8 + - - -
42A GLN* 3.2 46.0 + - - +
43A ALA* 3.2 31.3 + - - +
45A ILE* 1.3 87.6 - - + +
47A ALA* 1.3 56.9 + - - +
49A GLU* 3.5 9.6 + - - +
50A ARG* 3.0 52.2 + - - +
60D ARG* 5.1 8.9 - - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA 3.0 15.0 + - - +
44A CYS 3.8 1.8 - - - +
46A ARG* 1.3 74.4 - - - +
48A CYS* 1.3 60.6 + - - +
50A ARG* 3.4 24.3 - - - +
51A TYR* 2.8 30.2 + - - +
111A LEU* 5.2 0.9 - - - +
114A GLU* 4.1 6.1 - - + +
115A CYS* 4.0 19.0 - - - +
118A ALA* 3.8 23.1 - - + -
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Residues in contact with CYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A CYS* 3.0 24.8 + - - +
45A ILE 3.6 3.8 - - - +
47A ALA* 1.3 78.6 - - - +
49A GLU* 1.3 52.5 + - - +
51A TYR* 3.2 8.0 + - - +
52A LEU* 2.7 39.2 + - - +
66A ALA* 3.6 30.1 - - + +
69A CYS* 3.9 24.9 - - - -
70A ALA* 4.1 8.7 - - + -
115A CYS* 3.9 19.1 - - - -
119A CYS* 4.0 7.0 - - - -
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 2.8 31.0 + - - +
46A ARG* 4.0 10.9 - - - +
48A CYS* 1.3 70.0 - - - +
50A ARG* 1.3 56.0 + - - +
52A LEU* 3.2 12.8 + - + +
53A ALA* 2.7 37.5 + - - +
70A ALA* 4.8 11.8 - - + +
74A ARG* 3.2 31.7 + - - -
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 4.7 1.4 + - - -
46A ARG* 3.0 40.9 + - - +
47A ALA* 3.4 31.1 - - - +
49A GLU* 1.3 73.6 - - - +
51A TYR* 1.3 58.0 + - - +
54A LEU* 2.6 59.9 + - + +
111A LEU* 4.2 16.6 - - + +
114A GLU* 5.5 10.5 + - - +
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA 2.8 19.0 + - - +
48A CYS* 3.3 6.5 - - - +
50A ARG* 1.3 76.7 - - - +
52A LEU* 1.3 66.8 + - - +
55A CYS* 3.1 59.8 + - + +
57A GLU 5.0 0.5 + - - -
58A SER* 3.6 20.7 + - - -
62A GLN* 3.0 48.4 + - - +
63A ARG* 4.5 2.0 - - - -
66A ALA* 3.7 17.5 - - + -
105A CYS* 3.5 26.8 - - + -
111A LEU* 3.9 22.2 - - - +
112A GLU* 3.9 14.5 + - + +
115A CYS* 4.1 12.6 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A CYS 2.7 22.4 + - - +
49A GLU* 3.2 14.6 + - + +
51A TYR* 1.3 76.5 - - - +
53A ALA* 1.3 57.4 + - - +
55A CYS 5.2 2.4 - - - +
58A SER* 6.1 0.3 - - - -
63A ARG* 3.3 59.6 - - + +
66A ALA* 4.2 7.6 - - + +
67A GLY* 3.9 24.7 - - - +
70A ALA* 5.4 2.2 - - + -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU 2.7 21.7 + - - +
50A ARG* 4.8 0.2 - - - -
52A LEU* 1.3 76.1 - - - +
54A LEU* 1.3 74.5 + - + +
55A CYS 5.5 0.4 - - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 2.6 55.4 + - + +
53A ALA* 1.3 91.2 - - + +
55A CYS* 1.3 59.0 + - - +
56A THR* 2.7 16.3 + - - +
111A LEU* 3.4 23.5 - - + +
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Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG 3.9 0.2 + - - -
51A TYR* 3.1 39.5 + - + +
52A LEU 5.2 2.4 - - - +
54A LEU* 1.3 74.1 - - - +
56A THR* 1.3 66.1 + - - +
57A GLU* 3.6 25.6 - - - -
58A SER* 3.4 15.6 - - - -
109A GLU* 3.8 13.5 - - - -
111A LEU* 3.3 17.4 - - + +
112A GLU* 3.8 28.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il